Background
A useful workflow with dimensionality reduction (DR) is to be able to concatenate samples to view the consensus map for the completed DR analysis instead of visualizing each file separately.
Currently in Cytobank there isn't a way to permanently or temporarily concatenate files to facilitate this workflow, except in the case of Colored Overlay Dot Plots, which allow the temporary concatenation of any group of events and results in the uniform coloring of each group.
Suggested Workflow
If it is desired to concatenate files for analysis purposes other than colored overlay dot plots, our recommendation is to run DR and then concatenate the resulting files after the DR run is complete. We do not recommend concatenating the files before the run, then including the concatenated and separated files simultaneously in the same DR analysis. This strategy is ill-advised because it will make the run time of the algorithm longer and may negatively affect results. Concatenating the results of a DR after the run has completed is the proper way to accomplish the same workflow.
Use the FCS Concatenation Tool to concatenate DR result files after first downloading them. Afterwards, upload the concatenated result file into the DR experiment alongside the original result files.